Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Protein-protein interaction panel using mouse full-length cDNAs

We have developed a novel assay system for systematic analysis of protein-protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay system based on the mammalian two-hybrid method. Using gene-specific primers, we successfully constructed the assay samples by two rounds of PCR with up to 3.6 kb from the first-round PCR fragments. In the assay system, we designed all the steps to be performed by adding only samples, reagents, and cells into 384-well assay plates using two types of semiautomatic multiple dispensers. The system enabled us examine more than 20,000 assay wells per day. We detected 145 interactions in our pilot study using 3500 samples derived from mouse full-length enriched cDNAs. Analysis of the interaction data showed both several significant interaction clusters and predicted functions of a few uncharacterized proteins. In combination with our comprehensive mouse full-length cDNA clone bank covering a large part of the whole genes, our high-throughput assay system will discover many interactions to facilitate understanding of the function of uncharacterized proteins and the molecular mechanism of crucial biological processes, and also enable completion of a rough draft of the entire PPI panel in certain cell types or tissues of mouse within a short time.

[The long-term perfusion system on amylase release from dispersed acinar cells--comparative study with direct incubation techinique and residual stimulation]

We have modified the perfused guinea pig pancreatic acini system in order to obtain reproducible results in repeated secretagogue stimulation. No signs of tachyphylaxis were observed when cholecystokinin-8 (CCK-8) was administered as short pulse for 5 minutes and the interval between administrations were kept more than 90 minutes. Maximal amylase response was obtained at 10(-8) M of CCK-8 and a supra-maximal significant inhibition on amylase release was observed with higher doses of CCK-8. Twenty minutes stimulation with 10(-8) M of CCK-8 showed a biphasic response; while, 5 minutes stimulation showed a mono-phasic pattern. The results suggest that amylase response was highly influenced not only by the concentration of the secretagogue but also the duration of the stimulation in this perfusion system. The mechanism of this phenomenon may be comprehensive by the double-ligand-complex theory based on low and high affinity site on cell surface receptors.